chr10-90896315-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_006413.5(RPP30):c.620G>C(p.Gly207Ala) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000204 in 1,613,830 control chromosomes in the GnomAD database, with no homozygous occurrence. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G207D) has been classified as Uncertain significance.
Frequency
Consequence
NM_006413.5 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RPP30 | NM_006413.5 | c.620G>C | p.Gly207Ala | missense_variant, splice_region_variant | 10/11 | ENST00000371703.8 | |
RPP30 | NM_001104546.2 | c.620G>C | p.Gly207Ala | missense_variant, splice_region_variant | 10/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RPP30 | ENST00000371703.8 | c.620G>C | p.Gly207Ala | missense_variant, splice_region_variant | 10/11 | 1 | NM_006413.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152218Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251230Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135770
GnomAD4 exome AF: 0.0000198 AC: 29AN: 1461612Hom.: 0 Cov.: 30 AF XY: 0.0000234 AC XY: 17AN XY: 727142
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152218Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74360
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 27, 2022 | The c.620G>C (p.G207A) alteration is located in exon 10 (coding exon 10) of the RPP30 gene. This alteration results from a G to C substitution at nucleotide position 620, causing the glycine (G) at amino acid position 207 to be replaced by an alanine (A). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at